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This page was generated on 2021-11-24 15:06:06 -0500 (Wed, 24 Nov 2021).

CHECK results for intansv on machv2

To the developers/maintainers of the intansv package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/intansv.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 938/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
intansv 1.34.0  (landing page)
Wen Yao
Snapshot Date: 2021-11-23 04:15:06 -0500 (Tue, 23 Nov 2021)
git_url: https://git.bioconductor.org/packages/intansv
git_branch: RELEASE_3_14
git_last_commit: 499d4d8
git_last_commit_date: 2021-10-26 12:09:02 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: intansv
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:intansv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings intansv_1.34.0.tar.gz
StartedAt: 2021-11-23 17:48:54 -0500 (Tue, 23 Nov 2021)
EndedAt: 2021-11-23 17:57:22 -0500 (Tue, 23 Nov 2021)
EllapsedTime: 508.0 seconds
RetCode: 0
Status:   OK  
CheckDir: intansv.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:intansv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings intansv_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/intansv.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘intansv/DESCRIPTION’ ... OK
* this is package ‘intansv’ version ‘1.34.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘intansv’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DellyCluster: no visible global function definition for 'subjectHits'
LumpyCluster: no visible global function definition for 'subjectHits'
PindelCluster: no visible global function definition for 'subjectHits'
breakDancerCluster: no visible global function definition for
  'subjectHits'
mergeOLCNVs: no visible global function definition for 'subjectHits'
methodsMerge: no visible global function definition for 'subjectHits'
plotChromosome: no visible global function definition for 'queryHits'
plotChromosome: no visible global function definition for 'subjectHits'
plotChromosome: no visible global function definition for
  'seqlengths<-'
plotChromosome: no visible global function definition for 'seqlengths'
plotChromosome: no visible global function definition for 'aes'
plotRegion: no visible global function definition for 'seqlengths<-'
plotRegion: no visible global function definition for 'subjectHits'
plotRegion: no visible global function definition for 'aes'
plotRegion: no visible binding for global variable 'name'
readCnvnator: no visible global function definition for 'subjectHits'
readDelly: no visible global function definition for 'subjectHits'
readLumpy: no visible global function definition for 'subjectHits'
readPindel: no visible global function definition for 'subjectHits'
readSoftSearch: no visible global function definition for 'subjectHits'
readSvseq: no visible global function definition for 'subjectHits'
readSvseq : <anonymous>: no visible global function definition for
  'subjectHits'
softSearchCluster: no visible global function definition for
  'subjectHits'
tellOLPercantage: no visible global function definition for 'queryHits'
tellOLPercantage: no visible global function definition for
  'subjectHits'
Undefined global functions or variables:
  aes name queryHits seqlengths seqlengths<- subjectHits
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
methodsMerge   45.774  0.432  46.272
plotChromosome  9.611  0.033   9.652
plotRegion      8.515  0.057   8.580
readLumpy       6.215  0.014   6.237
readDelly       5.821  0.010   5.836
readPindel      5.038  0.014   5.058
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/intansv.Rcheck/00check.log’
for details.



Installation output

intansv.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL intansv
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘intansv’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (intansv)

Tests output


Example timings

intansv.Rcheck/intansv-Ex.timings

nameusersystemelapsed
methodsMerge45.774 0.43246.272
plotChromosome9.6110.0339.652
plotRegion8.5150.0578.580
readBreakDancer2.3270.0052.333
readCnvnator1.1510.0031.154
readDelly5.8210.0105.836
readLumpy6.2150.0146.237
readPindel5.0380.0145.058
readSoftSearch0.6680.0030.672
readSvseq0.6280.0020.630
svAnnotation2.6950.0142.715